Enzymes and Reaction Kinetics

Flashcards based on a lecture about enzymes, thermodynamics of chemical reactions, and enzyme kinetics for CHEM 4211 Biochemistry.

What are two main roles of enzymes in the body?

Enzymes are the builders and breakers in the body.

Why are enzymes important in pharmacology?

The majority of pharmaceutical drugs are small molecules that bind and either activate or inhibit enzyme activity.

What is the main purpose of an enzyme?

To speed up a chemical reaction in the body (making or breaking covalent bonds).

What is the reactant in an enzyme reaction called?

The substrate.

What is a common suffix for enzyme names?

-ase

What is the active site of an enzyme?

It is where the enzyme binds its substrate.

What are cofactors and why are they important for some enzymes?

Cofactors are small molecules that some enzymes require for activity.

What is a prosthetic group?

A tightly bound cofactor.

What are the two main classes of cofactors?

Coenzymes (organic molecules derived from vitamins) and metals.

What is a holoenzyme?

An enzyme with its cofactor.

What is an apoenzyme?

An enzyme without its cofactor.

Why are enzymes described as 'specific'?

They do their intended role without making side products.

Can enzymes be regulated?

Yes, enzymes can be regulated, which is important for control of cell behavior.

Can an enzyme be used multiple times?

Yes, since the enzyme is a catalyst, it can be used over and over again to catalyze a reaction.

Which class of enzymes catalyzes oxidation–reduction reactions?

Oxidoreductases

Which class of enzymes moves functional groups between molecules?

Transferases

Which class of enzymes cleaves bonds with the addition of water?

Hydrolyases

Which class of enzymes removes atoms to form double bonds or adds atoms to double bonds?

Lyases

Which class of enzymes moves functional groups within a molecule?

Isomerases

Which class of enzymes joins two molecules at the expense of ATP?

Ligases

Which enzyme catalyzes the reaction of adding a molecule of water to carbon dioxide in red blood cells?

Carbonic anhydrase

What type of enzyme is trypsin?

A proteolytic enzyme, meaning it catalyzes the hydrolysis of peptide bonds.

After which amino acids does trypsin specifically cleave peptide bonds?

Lysine or arginine.

In the reaction where DNA polymerase catalyzes the synthesis of DNA from free nucleotides, with magnesium ions initiating catalysis, what acts as the enzyme, substrate, and cofactor?

DNA polymerase is the enzyme, free nucleotides are the substrate, and magnesium ion is the cofactor.

What does a negative change in free energy (ΔG) indicate about a reaction?

The reaction is spontaneous, exergonic (releases free energy), and product formation is favored.

What is an exergonic reaction?

A reaction that releases free energy, having a negative ΔG.

What does a positive change in free energy (ΔG) indicate about a reaction?

The reverse reaction is spontaneous, the reaction is endergonic (gains free energy), and reactant formation is favored.

What is an endergonic reaction?

A reaction that gains free energy, having a positive ΔG.

What does a ΔG of zero mean for a reaction?

The reaction is at equilibrium, with no net formation of products or reactants.

What is the equation for the change in free energy (ΔG)?

ΔG = ΔG° + RTln([C]ᶜ[D]ᵈ / [A]ᵃ[B]ᵇ)

What are the standard state conditions for ΔG°?

1 mole reactants are converted to 1 mole products (or all species at 1M), 25⁰C (298K), and 1 atm pressure.

What is the difference between ΔG° and ΔG°'?

ΔG° is the standard free energy change at pH 0 ([H+]=1M), while ΔG°' is the biological standard free energy change at pH 7 ([H2O]=55.5 M).

What is the relationship between the standard biological free energy change (ΔG°') and the equilibrium constant (K'eq)?

ΔG°' = -RTln K'eq

If K'eq < 1, what does this tell you about ΔG°' and the equilibrium position?

ΔG°' will be positive (endergonic), and the equilibrium lies to the left (reactants are favored).

If K'eq > 1, what does this tell you about ΔG°' and the equilibrium position?

ΔG°' will be negative (exergonic), and the equilibrium lies to the right (products are favored).

If K'eq = 1, what does this tell you about ΔG°'?

ΔG°' = 0, meaning the reaction doesn’t favor reactants or products at equilibrium under standard biological conditions.

Can enzymes alter the reaction equilibrium?

No, enzymes cannot alter the reaction equilibrium; it is determined only by the free energy difference between products and reactants.

Given A → B with ΔG°’ = –10 kJ mol–1 and C → D with ΔG°’ = +10 kJ mol–1, which reaction will take place spontaneously under standard biological conditions?

A → B will take place spontaneously because it has a negative ΔG°’.

What determines whether a reaction will favor products or reactants?

The change in free energy (ΔG).

What determines the speed (kinetics) of a reaction?

The activation energy (ΔG‡).

Do enzymes change the final concentrations of products and reactants?

No, the enzyme doesn’t change the final concentrations of products and reactants; it only speeds up the rate at which equilibrium is reached.

What is the activation energy (ΔG‡)?

It is the extra energy needed to reach the high-energy transition state between the substrate and the product.

How do enzymes affect the activation energy?

Enzymes lower the activation energy (ΔG‡).

What type of molecule can inhibit proline racemase by binding similarly to the transition state structure?

A transition state analog inhibitor.

How does an enzyme's active site bind its substrate?

The enzyme active site is a unique 3D environment that specifically binds the substrate through several non-covalent interactions.

According to the 'induced fit' model, how do enzymes change when they bind their substrate?

The enzyme changes shape (conformation) when it binds the substrate.

How do enzymes relate to reaction speed and activation energy (ΔG‡)?

Enzymes speed up reactions by lowering the activation energy (ΔG‡), allowing the reaction to proceed more quickly to equilibrium.

How does the change in free energy (ΔG and ΔG°') relate to reaction spontaneity and equilibrium concentrations?

ΔG determines spontaneity (negative ΔG means spontaneous), while ΔG°' (standard biological free energy change) dictates the equilibrium constant (K'eq) and thus whether reactants or products are favored at equilibrium under standard biological conditions.